Inference of Self-Regulated Transcriptional Networks by Comparative Genomics

Joseph P. Cornish, Fialelei Matthews, Julien R. Thomas, Ivan Erill
2012 Evolutionary Bioinformatics  
The assumption of basic properties, like self-regulation, in simple transcriptional regulatory networks can be exploited to infer regulatory motifs from the growing amounts of genomic and meta-genomic data. These motifs can in principle be used to elucidate the nature and scope of transcriptional networks through comparative genomics. Here we assess the feasibility of this approach using the SOS regulatory network of Gram-positive bacteria as a test case. Using experimentally validated data, we
more » ... show that the known regulatory motif can be inferred through the assumption of self-regulation. Furthermore, the inferred motif provides a more robust search pattern for comparative genomics than the experimental motifs defined in reference organisms. We take advantage of this robustness to generate a functional map of the SOS response in Gram-positive bacteria. Our results reveal definite differences in the composition of the LexA regulon between Firmicutes and Actinobacteria, and confirm that regulation of cell-division inhibition is a widespread characteristic of this network among Gram-positive bacteria.
doi:10.4137/ebo.s9205 pmid:23032607 pmcid:PMC3422134 fatcat:sfeawknmhrcmnpaigtjps6igny